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Replace references to python obographs with OAK. Fixes #4.
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pkalita-lbl committed Jul 7, 2022
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Expand Up @@ -33,13 +33,6 @@ og2dot simple-og.json > test.dot
dot test.dot -Tpng -Grankdir=BT > test.png
```

Command line; from [python obographs package](https://github.com/biolink/biolink-api/tree/master/obographs)

```bash
ogr -p subClassOf BFO:0000050 -r obo:go -t png g nucleus
```


### API

```javascript
Expand Down Expand Up @@ -268,25 +261,19 @@ As well as configuring via style sheets, an individual node or edge can configur
```


## Obographs python

See:

https://github.com/biolink/biolink-api/tree/master/obographs

(note: this python API may move to its own repo in future)
## Ontology Access Kit

obographs-python command line:
This library is integrated into [Ontology Access Kit (OAK)](https://github.com/INCATools/ontology-access-kit) to support its [`viz` subcommand](https://incatools.github.io/ontology-access-kit/cli.html#runoak-viz). For example:

```bash
ogr -p subClassOf BFO:0000050 -r go -t png a nucleus
runoak -i ontobee: viz HP:0000787
```

This proceeds by:

1. Using the python obographs library to extract a networkx subgraph around the specified node
1. Using the [python oaklib library](https://incatools.github.io/ontology-access-kit/intro/tutorial02.html) to extract a subgraph around the specified node
2. Write as obographs-json
3. Calls og2dot.js
3. Calls og2dot

## Use from biolink-api REST

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